RetrogeneDB ID: | retro_cfam_1684 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:17145310..17145992(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SSBP3 | ||
| Ensembl ID: | ENSCAFG00000019045 | ||
| Aliases: | None | ||
| Description: | single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674] |
Retrocopy-Parental alignment summary:
>retro_cfam_1684
CCCCAGGCCCCCATCAGAATGGGAAACCAGCCTCCGGGAGGAGTTCCTGGGACCCAGCGGTTGCAGCCCAATTCTATGGA
TCCCACCCGACAACAAGGGCACCCCAACCTGGGAGGATCGATGAGAGAATGAACCCTCCCCGAGGCATGGGGCCCATGGG
GCCTGGCCCACAGCATTACGGCAGCGGCATGAGACCACCACGCAACTCCCTCGGCCCGCCATGCCCGGGGGTGACATGGG
CCCGGGAGCTGGCAGGCCCTGGCCAGATCCCAACAGTGCTAACTCAACTCCTTACTCCTCCTCATCACCTGGTACCTACG
TGGGACCTCCTGGTGGTGGCCCCCCAGGAACACCCATCATGCTTAGTCCTGCAGATTTAACAAATTCCAGTGACAGCATC
TACACCATGATTAATCCGGTGCCGCCTGGAGGCAGCCGGTCCAACTTCCCCATGGGTCCAGGCTCGCACGGCCGGATGGA
AGGCATGGGCGGCATGGAGCCACACCACATGAACGGATCGTTAGGGTCAGGTGACATAGATGGACTTCCCAAAAATTCTT
CTAACAACATAAGTGGCATTAGCAATCCTCCAGGCACCCCTTGAGACGATGGCGATCTAGGAGAGAACTTCCTCCACTCC
TTCCAGAATGACAATTTTTCTCCAAGCATGAGGATGAGCATG
ORF - retro_cfam_1684 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.28 % |
| Parental protein coverage: | 82.97 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PSSMMGPHSQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSM-QRMNPPRGMGPMGPGPQNYGSGMRPPPN |
| P........QPPGGVPGTQ.L.PNSMDPTRQQGHPN.GGSM..RMNPPRGMGPMGPGPQ.YGSGMRPP.N | |
| Retrocopy | PQAPIRMGNQPPGGVPGTQRLQPNSMDPTRQQGHPNLGGSM<ERMNPPRGMGPMGPGPQHYGSGMRPPRN |
| Parental | SLGP-AMPGINMGPGAGRPWPNPNSANSIPYSSSSPGTYVGPPGGGGPPGTPIMPSPADSTNSSDNIYTM |
| SLGP.AMPG..MGPGAGRPWP.PNSANS.PYSSSSPGTYVGPPGGG.PPGTPIM.SPAD.TNSSD.IYTM | |
| Retrocopy | SLGP<AMPGGDMGPGAGRPWPDPNSANSTPYSSSSPGTYVGPPGGG-PPGTPIMLSPADLTNSSDSIYTM |
| Parental | INPVPPGGSRSNFPMGPGSDGPMGGMGGMEPHHMNGSLGSGDIDGLPKNSPNNISGISNPPGTPRDDGEL |
| INPVPPGGSRSNFPMGPGS.G.M.GMGGMEPHHMNGSLGSGDIDGLPKNS.NNISGISNPPGTP.DDG.L | |
| Retrocopy | INPVPPGGSRSNFPMGPGSHGRMEGMGGMEPHHMNGSLGSGDIDGLPKNSSNNISGISNPPGTP*DDGDL |
| Parental | GGNFLHSFQNDNYSPSMTMSV |
| G.NFLHSFQNDN.SPSM.MS. | |
| Retrocopy | GENFLHSFQNDNFSPSMRMSM |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP012049_cerebellum | 0 .04 RPM | 169 .42 RPM |
| SRP017611_brain | 0 .24 RPM | 139 .97 RPM |
| SRP017611_kidney | 0 .00 RPM | 25 .09 RPM |
| SRP017611_liver | 0 .00 RPM | 12 .40 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1684 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1684 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1684 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000019045 | 1 retrocopy |
retro_cfam_1684 ,
|
| Echinops telfairi | ENSETEG00000000453 | 1 retrocopy |